def test_calc_dAdt_ccd_fmm(self):
try:
import fmm3dpy
except ImportError:
print('skiping test, no fmm3dpy')
return
with open('test.ccd', 'w') as f:
f.write('# number of elements\n')
f.write('2\n')
f.write('0e-000 0e-000 0e-000 0e+000 0e+000 1e-000\n')
f.write('0e-000 0e-000 0e-000 0e+000 1e+000 0e-000\n')
msh = mesh_io.Msh()
# milimeters
msh.nodes = mesh_io.Nodes(
np.array([[1e3, 0., 0.], [0., 1e3, 0.], [0, 0., 1e3],
[0., 0., -1e3]]))
coil_matrix = np.eye(4)
dadt = coil._calculate_dadt_ccd_FMM(msh, 'test.ccd', coil_matrix, 1e6,
None)
assert np.allclose(
dadt[:],
np.array([[0., 0.1, -0.1], [-0.1, 0, 0], [0.1, 0., 0.],
[-0.1, 0., 0.]]))
os.remove('test.ccd')
def test_calc_dAdt_ccd(self):
with open('test.ccd', 'w') as f:
f.write('# number of elements\n')
f.write('2\n')
f.write('0e-000 0e-000 0e-000 0e+000 0e+000 1e-000\n')
f.write('0e-000 0e-000 0e-000 0e+000 1e+000 0e-000\n')
msh = mesh_io.Msh()
# milimeters
msh.nodes = mesh_io.Nodes(np.array([[1e3, 0., 0.], [0., 1e3, 0.], [0, 0., 1e3]]))
coil_matrix = np.eye(4)
dadt = coil._calculate_dadt_ccd(msh, 'test.ccd', coil_matrix, 1e6, None)
assert np.allclose(dadt[[1, 2, 3]], np.array([[0., 0.1, -0.1],
[-0.1, 0, 0],
[0.1, 0., 0.]]))
os.remove('test.ccd')
def test_build_electrode_on_mesh(self):
''' Idea: Function to build a simple electrode (with holes) '''
X, Y, Z = np.meshgrid(np.linspace(-8, 8, 17, dtype=float),
np.linspace(-8, 8, 17, dtype=float),
0)
nodes = np.vstack([X.reshape(-1), Y.reshape(-1), Z.reshape(-1)]).T
poly = np.array([[5, 5], [5, -5], [-5, -5], [-5, 5]])
h = 5
c = [0, 0, 0]
ydir = [0, 1, 0]
tri = scipy.spatial.Delaunay(nodes[:, :2])
mesh = mesh_io.Msh()
mesh.elm = mesh_io.Elements(triangles=tri.simplices+1)
mesh.nodes = mesh_io.Nodes(nodes)
w_elec = electrode_placement._build_electrode_on_mesh(c, ydir, poly, h, mesh, el_vol_tag=2,
el_surf_tag=1002, on_top_of=1)
#mesh_io.write_msh(w_elec, '~/Tests/electrode.msh')
vols = w_elec.elements_volumes_and_areas().value
assert np.isclose(vols[w_elec.elm.tag1 == 2].sum(), 100 * h)
assert np.isclose(vols[w_elec.elm.tag1 == 1002].sum(), 100)
h = [5, 3]
mesh = mesh_io.Msh()
mesh.elm = mesh_io.Elements(triangles=tri.simplices+1)
mesh.nodes = mesh_io.Nodes(nodes)
w_elec = electrode_placement._build_electrode_on_mesh(c, ydir, poly, h,
copy.deepcopy(mesh),
el_vol_tag=[2, 3],
el_surf_tag=[1002, 1003], on_top_of=1)
vols = w_elec.elements_volumes_and_areas().value
assert np.isclose(vols[w_elec.elm.tag1 == 2].sum(), 100 * 5)
assert np.isclose(vols[w_elec.elm.tag1 == 3].sum(), 100 * 3)
assert np.isclose(vols[w_elec.elm.tag1 == 1002].sum(), 100)
assert np.isclose(vols[w_elec.elm.tag1 == 1003].sum(), 100)
plug = np.array([[2, 2], [2, -2], [-2, -2], [-2, 2]])
w_elec = electrode_placement._build_electrode_on_mesh(c, ydir, poly, h,
copy.deepcopy(mesh),
el_vol_tag=[2, 3],
el_surf_tag=[1002, 1003],
on_top_of=1,
plug=plug,
plug_tag=2003)
vols = w_elec.elements_volumes_and_areas().value
assert np.isclose(vols[w_elec.elm.tag1 == 2].sum(), 100 * 5)
assert np.isclose(vols[w_elec.elm.tag1 == 3].sum(), 100 * 3)
assert np.isclose(vols[w_elec.elm.tag1 == 1002].sum(), 100)
assert np.isclose(vols[w_elec.elm.tag1 == 1003].sum(), 100)
assert np.isclose(vols[w_elec.elm.tag1 == 2003].sum(), 16)
h = [5, 3, 1]
middle_layer = np.array([[2, 2], [2, -2], [-2, -2], [-2, 2]])
mesh = mesh_io.Msh()
mesh.elm = mesh_io.Elements(triangles=tri.simplices+1)
mesh.nodes = mesh_io.Nodes(nodes)
w_elec = electrode_placement._build_electrode_on_mesh(c, ydir, poly, h,
copy.deepcopy(mesh),
el_vol_tag=[2, 3],
el_surf_tag=[1002, 1003],
on_top_of=1,
middle_layer=middle_layer)
vols = w_elec.elements_volumes_and_areas().value
assert np.isclose(vols[w_elec.elm.tag1 == 2].sum(), 100 * 6 + (100 - 16) * 3)
assert np.isclose(vols[w_elec.elm.tag1 == 3].sum(), 16 * 3)
assert np.isclose(vols[w_elec.elm.tag1 == 1002].sum(), 100)
assert np.isclose(vols[w_elec.elm.tag1 == 1003].sum(), 16)
meshfile = os.path.join(sub_dir, sub, sub + '.msh') m2mfile = os.path.join(sub_dir, sub, 'm2m_' + sub) outfile = os.path.join(sub_dir, sub, 'simnibs_simulation') intFile = os.path.join(sub_dir, sub, 'tms_int_' + sub + '.txt') coordFile = os.path.join(sub_dir, sub, 'coordinates_' + sub + '.txt') tint = np.loadtxt(intFile).astype(float) coord = np.loadtxt(coordFile).astype(float)[1:].tolist()[0] # Initalize a session s = sim_struct.SESSION() s.fnamehead = meshfile s.subpath = m2mfile s.pathfem = outfile mesh = mesh_io.Msh(fn=s.fnamehead) # Initialize a list of TMS simulations tmslist = s.add_tmslist() tmslist.fnamecoil = coilnifti tmslist.anisotropy_type = 'scalar' # Initialize a TEMPORARY coil position to get params pos = tmslist.add_position() pos.centre = coord # entry coordinates pos.distance = 1. # coil distance (mm) pos.didt = tint * 1e6 # TMS intensity (A/s) pos.pos_ydir = ([1, 0, 0]) # coil towards right pos.calc_matsimnibs(mesh) # scalp projection pos.pos_ydir = (pos.matsimnibs[0:3, 3] + [1, 0, 0]).tolist()
def test_build_electrode(self):
X, Y = np.meshgrid(np.linspace(-8, 8, 17, dtype=float), np.linspace(-8, 8, 17, dtype=float))
nodes = np.vstack([X.reshape(-1), Y.reshape(-1)]).T
tri = scipy.spatial.Delaunay(nodes)
poly = np.array([[5, 5], [5, -5], [-5, -5], [-5, 5]])
trs = tri.simplices[:, [1,0,2]]
#hole = [np.array([[2, 2], [2, -2], [-2, -2], [-2, 2]])]
h = 5
new_points, tetrahedra, triangles, _, _, _, _ = electrode_placement._build_electrode(
poly, h, tri.points, trs)
mesh = mesh_io.Msh()
mesh.elm = mesh_io.Elements(#triangles=triangles+1)
tetrahedra=tetrahedra + 1)
mesh.nodes = mesh_io.Nodes(new_points)
#mesh_io.write_msh(mesh, '~/Tests/electrode.msh')
m = new_points[tetrahedra[:, 1:]] -\
new_points[tetrahedra[:, 0]][:, None, :]
vol = -np.linalg.det(m) / 6.0
assert np.isclose(np.sum(vol), 100 * h)
sides = new_points[triangles[:, 1:]] - \
new_points[triangles[:, 0]][:, None, :]
n = np.cross(sides[:, 0], sides[:, 1])
area = np.linalg.norm(n, axis=1) * 0.5
assert np.isclose(np.sum(area), 100)
#assert np.isclose(np.sum(area), 2 * 100 + 4 * 50)
h = [3, 1]
new_points, tetrahedra, triangles, _, _, th_tags, tr_tags = electrode_placement._build_electrode(
poly, h, tri.points, trs)
mesh = mesh_io.Msh()
mesh.elm = mesh_io.Elements(#triangles=triangles+1)
tetrahedra=tetrahedra + 1)
mesh.elm.tag1 = th_tags + 1
mesh.elm.tag2 = th_tags + 1
mesh.nodes = mesh_io.Nodes(new_points)
#mesh_io.write_msh(mesh, '~/Tests/electrode.msh')
m = new_points[tetrahedra[:, 1:]] -\
new_points[tetrahedra[:, 0]][:, None, :]
vol = -np.linalg.det(m) / 6.0
assert np.isclose(np.sum(vol[th_tags==0]), 100 * 3)
assert np.isclose(np.sum(vol[th_tags==1]), 100 * 1)
mesh.elm = mesh_io.Elements(triangles=triangles+1)
#mesh_io.write_msh(mesh, '~/Tests/electrode.msh')
sides = new_points[triangles[:, 1:]] - \
new_points[triangles[:, 0]][:, None, :]
n = np.cross(sides[:, 0], sides[:, 1])
area = np.linalg.norm(n, axis=1) * 0.5
assert np.isclose(np.sum(area[tr_tags==0]), 100)
assert np.isclose(np.sum(area[tr_tags==1]), 100)
#assert np.isclose(np.sum(area[tr_tags==1]), 2 * 100 + 4 * 10)
#assert np.isclose(np.sum(area[tr_tags==0]), 2 * 100 + 4 * 30)
plug = np.array([[2, 2], [2, -2], [-2, -2], [-2, 2]])
new_points, tetrahedra, triangles, _, _, th_tags, tr_tags = electrode_placement._build_electrode(
poly, h, tri.points, trs, plug=plug)
sides = new_points[triangles[:, 1:]] - \
new_points[triangles[:, 0]][:, None, :]
n = np.cross(sides[:, 0], sides[:, 1])
area = np.linalg.norm(n, axis=1) * 0.5
assert np.isclose(np.sum(area[tr_tags==0]), 100)
assert np.isclose(np.sum(area[tr_tags==1]), 100)
#assert np.isclose(np.sum(area[tr_tags==0]), 2 * 100 + 4 * 30)
#assert np.isclose(np.sum(area[tr_tags==1]), 2 * 100 + 4 * 10 - 16)
assert np.isclose(np.sum(area[tr_tags==-1]), 16)
middle_layer = np.array([[2, 2], [2, -2], [-2, -2], [-2, 2]])
h = [3, 1, 3]
new_points, tetrahedra, triangles, _, _, th_tags, tr_tags = electrode_placement._build_electrode(
poly, h, tri.points, trs, middle_layer=middle_layer)
m = new_points[tetrahedra[:, 1:]] -\
new_points[tetrahedra[:, 0]][:, None, :]
vol = -np.linalg.det(m) / 6.0
assert np.isclose(np.sum(vol[th_tags==0]), 100 * 6 + (100-16) * 1)
assert np.isclose(np.sum(vol[th_tags==1]), 16 * 1)
sides = new_points[triangles[:, 1:]] - \
new_points[triangles[:, 0]][:, None, :]
n = np.cross(sides[:, 0], sides[:, 1])
area = np.linalg.norm(n, axis=1) * 0.5
assert np.isclose(np.sum(area[tr_tags==0]), 100)
assert np.isclose(np.sum(area[tr_tags==1]), 16)